.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH KISSREADS "1" "November 2014" "kissreads 1.2.6" "User Commands"
.SH NAME
kissreads \- manual page for kissreads 1.2.6
.SH DESCRIPTION
NAME
kissReads, version kissreads module 1.2.6 \- Copyright INRIA \- CeCILL License
.PP
SYNOPSIS
kissreads/kissreads <toCheck.fasta> <readsC1.fasta> [<readsC2.fasta> [<readsC3.fasta] ...] [\-k value] [\-c value] [\-d value] [\-O value] [\-o name] [\-u name] [\-n] [\-I] [\-i index_stride] [\-m align_file] [\-s] [\-f] [\-h]
.PP
DESCRIPTION
Checks for each sequence contained into the toCheck.fasta if
it is read coherent (each position is covered by at least "min_coverage" read(s)) with reads from readsA.fasta or readsB.fasta
A sequence s from toCheck is treated as follow:
.IP
if (s coherent with at least one read set): output the sequence as follows
.IP
>original fasta comment|C1:min<avg\-corr_avg<max|C2:min<avg\-cor_avg<max|C3...:
>s
.IP
With A:min<avg\-cor_avg<max standing for : value of the position having minimal coverage in readsA.fasta < average coverage in readsA.fasta \- R\-squarred corrected average in readsA.fa < value of the position having maximal coverage in readsA.fasta
The coverage is the number of reads that perfectly mapped a position
Any other situation (s not coherent with any): couple non read coherent, not outputed
.PP
OPTIONS
.HP
\fB\-k\fR size_seed: will use seeds of length size_seed. Default: 25.
.HP
\fB\-O\fR minimal_read_overlap: a read can be mapped if its overlap is a least "minimal_read_overlap". Default: k
.HP
\fB\-c\fR min_coverage: a sequence is covered by at least min_coverage coherent reads. Default: 2
.HP
\fB\-d\fR max_substitutions: Maximal number of substitutions authorized between a read and a fragment. Note that no substitution is allowed on the central position while anaylizing the kissnp output. Default: 1.
.HP
\fB\-o\fR file_name: write read\-coherent outputs. Default: standard output
.HP
\fB\-u\fR file_name: write unread\-coherent outputs. Default: standard output
.HP
\fB\-n\fR the input file (toCheck.fasta) is a kissnp output (incompatible with \fB\-I\fR option)
.IP
in this case: 1/ only the upper characters are considered (no mapping done on the extensions) and 2/ the central position (where the SNP occurs) is strictly mapped, no subsitution is authorized on this position.
.HP
\fB\-I\fR the input file (toCheck.fasta) is an Intl output (incompatible with \fB\-n\fR option)
.HP
\fB\-i\fR index_stride (int value). This is a heuristic for limiting the memory footprint. Instead of indexing each kmer of the sequences contained into the toCheck.fasta, kissreads indexes kmers occurring each "index_stride" position. Default = 1 (no heuristic)
.HP
\fB\-t\fR max number of threads (also limited by number of input files)
.HP
\fB\-m\fR align_file, write a file of reads mapped to sequences in file align_file
.HP
\fB\-s\fR silent mode
.HP
\fB\-f\fR outputs coherent events in a standard fasta file format
.HP
\fB\-h\fR prints this message and exit
.SH "SEE ALSO"
The full documentation for
.B kissreads
is maintained as a Texinfo manual.  If the
.B info
and
.B kissreads
programs are properly installed at your site, the command
.IP
.B info kissreads
.PP
should give you access to the complete manual.